Scientists know that the trillions of bacteria and other microbes that live in our guts play an important role in health, influencing our risk of developing obesity, heart disease, Type 2 diabetes and a wide range of other conditions. But now a large new international study has found that the composition of these microorganisms, collectively known as our microbiomes, is largely shaped by what we eat.

By analyzing the diets, health and microbiomes of more than a thousand people, researchers found that a diet rich in nutrient-dense, whole foods supported the growth of beneficial microbes that promoted good health. But eating a diet full of highly processed foods with added sugars, salt and other additives had the opposite effect, promoting gut microbes that were linked to worse cardiovascular and metabolic health.

The researchers found that what people ate had a more powerful impact on the makeup of their microbiomes than their genes. They also discovered that a variety of plant and animal foods were linked to a more favorable microbiome.

One critical factor was whether people ate foods that were highly processed or not. People who tended to eat minimally processed foods like vegetables, nuts, eggs and seafood were more likely to harbor beneficial gut bacteria. Consuming large amounts of juices, sweetened beverages, white bread, refined grains, and processed meats, on the other hand, was associated with microbes linked to poor metabolic health.

“It goes back to the age-old message of eating as many whole and unprocessed foods as possible,” said Dr. Sarah E. Berry, a nutrition scientist at King’s College London and a co-author of the new study, which was published Monday in Nature Medicine. “What this research shows for the first time is the link between the quality of the food we’re eating, the quality of our microbiomes and ultimately our health outcomes.”

The findings could one day help doctors and nutritionists prevent or perhaps even treat some diet-related diseases, allowing them to prescribe personalized diets to people based on the unique makeup of their microbiomes and other factors.

Many studies suggest that there is no one-size-fits-all diet that works for everyone. The new study, for example, found that while some foods were generally better for health than others, different people could have wildly different metabolic responses to the same foods, mediated in part by the kinds of microbes residing in their guts.

“What we found in our study was that the same diet in two different individuals does not lead to the same microbiome, and it does not lead to the same metabolic response,” said Dr. Andrew T. Chan, a co-author of the study and a professor of medicine at Harvard Medical School and Massachusetts General Hospital. “There is a lot of variation.”

The new findings stem from an international study of personalized nutrition called Predict, which is the world’s largest research project designed to look at individual responses to food. Started in 2018 by the British epidemiologist Tim Spector, the study has followed over 1,100 mostly healthy adults in the United States and Britain, including hundreds of identical and nonidentical twins.

The researchers collected data on a wide range of factors that influence metabolism and disease risk. They analyzed the participants’ diets, microbiomes and body fat. They took blood samples before and after meals to look at their blood sugar, hormones, cholesterol and inflammation levels. They monitored their sleep and physical activity. And for two weeks they had them wear continuous glucose monitors that tracked their blood sugar responses to different meals.

The researchers were surprised to discover that genetics played only a minor role in shaping a person’s microbiome. Identical twins were found to share just 34 percent of the same gut microbes, while people who were unrelated shared about 30 percent of the same microbes. The composition of each person’s microbiome appeared instead to be driven more by what they ate, and the types of microbes in their guts played a strong role in their metabolic health.

The researchers identified clusters of so-called good gut bugs, which were more common in people who ate a diverse diet rich in high-fiber plants — like spinach, broccoli, tomatoes, nuts and seeds — as well as minimally processed animal foods such as fish and full-fat yogurt. They also found clusters of “bad” gut bugs that were common in people who regularly consumed foods that were highly processed. One common denominator among heavily processed foods is that they tend to contain very little fiber, a macronutrient that helps to nourish good microbes in the gut, the researchers said.

Among the “good” strains of gut microbes were Prevotella copri and Blastocystis, both of which were associated with lower levels of visceral fat, the kind that accumulates around internal organs and that increases the risk of heart disease. These microbes also appeared to improve blood sugar control, an indicator of diabetes risk. Other beneficial microbes were associated with reduced inflammation and lower spikes in blood fat and cholesterol levels after meals, all of which play a role in cardiovascular health.

The new study was funded and supported by Zoe Global, a health science company, as well as by the Wellcome Trust, a British nonprofit, and several public health groups.

Dr. Berry said the findings suggest that by looking at microbiome profiles they can identify people at high risk of developing metabolic diseases and intervene early on. She and her colleagues are now planning a clinical trial that will test whether telling people to change specific foods in their diets can alter levels of good and bad microbes in their guts and subsequently improve their health.

“We think there are lots of small changes that people can make that can have a big impact on their health that might be mediated through the microbiome,” she said.

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